.. _scil_dwi_extract_b0:

scil_dwi_extract_b0
===================

::

	usage: __main__.py [-h] [--all | --mean | --cluster-mean | --cluster-first]
	                   [--block-size INT] [--single-image] [--b0_threshold thr]
	                   [--skip_b0_check] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec out_b0
	
	Extract B0s from DWI, based on the bval and bvec information.
	
	The default behavior is to save the first b0 of the series.
	
	positional arguments:
	  in_dwi                DWI Nifti image.
	  in_bval               b-values filename, in FSL format (.bval).
	  in_bvec               b-values filename, in FSL format (.bvec).
	  out_b0                Output b0 file(s).
	
	options:
	  -h, --help            show this help message and exit
	  --block-size INT, -s INT
	                        Load the data using this block size. Useful
	                        when the data is too large to be loaded in memory.
	  --single-image        If output b0 volume has multiple time points, only outputs a single 
	                        image instead of a numbered series of images.
	  --b0_threshold thr    Threshold under which b-values are considered to be b0s.
	                        [Default: 20] 
	                        * Note. We would expect to find at least one b-value in the 
	                          range [0, b0_threshold]. To skip this check, use --skip_b0_check.
	  --skip_b0_check       By default, we supervise that at least one b0 exists in your data
	                        (i.e. b-values below the default --b0_threshold). Use this option to 
	                        allow continuing even if the minimum b-value is suspiciously high.
	                        If no b-value is found below the threshold, the script will continue 
	                        with your minimal b-value as new --b0_threshold.
	                        Use with care, and only if you understand your data.
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  -f                    Force overwriting of the output files.
	
	Options in the case of multiple b0s.:
	  --all                 Extract all b0s. Index number will be appended to the output file.
	  --mean                Extract mean b0.
	  --cluster-mean        Extract mean of each continuous cluster of b0s.
	  --cluster-first       Extract first b0 of each continuous cluster of b0s.
	
	2.2.2